ArticleGigaScience2020
A high-quality chromosomal genome assembly of Diospyros oleiferaCheng.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 68 citations in OpenAlex.
- Distinct genomic architectures but the same gene underlie the convergent evolution of a plant supergene.Science advances · 2026Article
- An evolutionary conserved CBL1-CIPK6 complex of oil persimmon involved in responses to ABA, salt and drought stress.BMC plant biology · 2025Article
- Haplotype-resolved and chromosome-level reference genome assembly ofHorticulture research · 2025Article
- Genetic insights into the dissolution of dioecy in diploid persimmon Diospyros oleifera Cheng.BMC plant biology · 2023Article
- Construction of a High-DensityInternational journal of molecular sciences · 2023Article
- Comparative Metabolomic and Transcriptomic Analyses Reveal Distinct Ascorbic Acid (AsA) Accumulation Patterns between PCA and PCNA Persimmon Developing Fruit.International journal of molecular sciences · 2023Article
- Population Genetic Analysis in Persimmons (Plants (Basel, Switzerland) · 2023Article
- Allele-aware chromosome-level genome assembly of the autohexaploid Diospyros kaki Thunb.Scientific data · 2023Article
- From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes.Scientific reports · 2023Article
- Full-length transcriptome profiling for fruit development in Diospyros oleifera using nanopore sequencing.BMC genomic data · 2023Article
- Regulatory mechanism ofFrontiers in plant science · 2023Article
- Investigating phenotypic relationships in persimmon accessions through integrated proteomic and metabolomic analysis of corresponding fruits.Frontiers in plant science · 2023Article
- Characterization and phylogenetic analysis of the complete mitochondrial genome sequence ofHeliyon · 2022Article
- Chromosome-Scale Genome Assembly of Gilia yorkii Enables Genetic Mapping of Floral Traits in an Interspecies Cross.Genome biology and evolution · 2022Article
- Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding.PloS one · 2022Article
- Genomics-based discrimination of 2n gamete formation mechanisms in polyploids: a case study in nonaploid Diospyros kaki 'Akiou'.G3 (Bethesda, Md.) · 2021Article
- Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb.BMC genomics · 2021Article
- A high-quality chromosomal genome assembly of Diospyros oleiferaCheng.GigaScience · 2020Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDiospyros oleifera Cheng, of the family Ebenaceae, is an economically important tree. Phylogenetic analyses indicate that D. oleifera is closely related to Diospyros kaki Thunb. and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and elucidate the molecular mechanisms of important traits.
findingsThe D. oleifera genome was assembled with 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was ∼812.3 Mb and had a high level of continuity with N50 of 3.36 Mb. Fifteen scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. Repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes were expanded in the D. oleifera genome compared with Diospyros lotus, Camellia sinensis, and Vitis vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient γ event, a second whole-genome duplication event occurred in D. oleifera and D. lotus.
conclusionsWe generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros.
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